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 6KM8 | pdb_00006km8

Crystal Structure of Momordica charantia 7S globulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.278 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition.

Kesari, P., Pratap, S., Dhankhar, P., Dalal, V., Mishra, M., Singh, P.K., Chauhan, H., Kumar, P.

(2020) Sci Rep 10: 1160-1160

  • DOI: https://doi.org/10.1038/s41598-020-58138-9
  • Primary Citation Related Structures: 
    6KM8

  • PubMed Abstract: 

    Momordica charantia (Mc) seeds are widely used edible crop with high nutritional quality. The food and pharmaceutical industries use it as a natural anti-oxygenic agent. Herein, a ~52 kDa protein, which is a major part of seed proteome has been purified, biochemically characterized and structure has been determined. MALDI-ESI-MS identified peptide fragments and contig-deduced sequence suggested the protein to be homologous to 7S globulins. The crystal structure shows that protein has a bicupin fold similar to 7S globulins and the electron density for a copper and acetate ligand were observed in the C-terminal barrel domain. In silico study reveals that a tripeptide (VFK) from Mc7S possess a higher binding affinity for angiotensin converting enzyme (ACE) than already reported drug Lisinopril (LPR). The protein is a glycoprotein and highly stable under varying thermal and pH conditions due to its secondary structures. The DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) assay showed the protein to have an anti-oxygenic nature and can aid in scavenging free radical from sample. The protein can assist to enhance the nutritional and functional value of food by acting as a food antioxidant. Further, characterization of Mc7S required which might add in importance of Mc7S as antioxidant, anti-diabetic and anti-hypertensive.


  • Organizational Affiliation: 
    • Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.

Macromolecule Content 

  • Total Structure Weight: 43.12 kDa 
  • Atom Count: 2,753 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 381 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7S globulin381Momordica charantiaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFM7 (Momordica charantia)
Explore A0A6I8WFM7 
Go to UniProtKB:  A0A6I8WFM7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6I8WFM7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.278 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.765α = 90
b = 90.765β = 90
c = 68.476γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description